NAMD Utilities

VMD (with its plugins and script library) is closely tied to NAMD and is used for:
- visualizing the initial structure and trajectory
- assembling biomolecular aggregates
- solvating the system in a membrane and/or water
- building the molecular structure (PSF file)
- visualizing and analyzing the trajectory
Tcl is used within NAMD and VMD to provide scripting capabilities.
FFTW may be compiled into NAMD for better PME performance.
X-PLOR and CHARMM are useful for setup and analysis.
The CHARMM parameters are available for use with NAMD.
Find CHARMM docs and forums at www.charmm.org and other useful info at http://brooks.scripps.edu/charmm_docs/charmm.htm.
The Cornell et al. (AMBER) parameters are available in CHARMM format for use with NAMD.
The OPLS parameters are available in CHARMM format for use with NAMD. OPLS requires the vdwGeometricSigma option, see NamdAndOPLS on the NamdWiki.
Alchemify by Jérôme Hénin prepares files for alchemical free energy calculations.

VMD plugins and script library
The namdplot csh script works with Grace to plot energies, etc. (This older version uses XMGR.)
VMD's new namdplot plugin works on Windows and has both text and graphical interfaces.
namdstats prints average energies, etc.
namdpstats print average on pressures for runs with outputPressure enabled.
namddat is a hack of namdplot to write data to a file
This front-end simplifies running NAMD and even works with our DQS setup.
These MATLAB scripts read and write DCD trajectory files.
Andriy Anishkin's scripts

Full examples, including structure building, are in the tutorials
ApoA1 benchmark (92,224 atoms, periodic, PME)
config, directory, 2.8M .tar.gz, 2.7M .zip
ApoA1 has been the standard NAMD cross-platform benchmark for years.
ATPase benchmark (327,506 atoms, periodic, PME)
config, directory, 26.9M .tar.gz, 26.9M .zip
STMV (virus) benchmark (1,066,628 atoms, periodic, PME)
config, directory, 27.5M .tar.gz, 27.5M .zip
STMV is useful for demonstrating scaling to thousands of processors.
tiny benchmark (507 atoms, periodic, PME)
config, directory, 33k .tar.gz, 32k .zip
This single-patch benchmark runs at about 14 ms per step and is representative of the workload of a single processor in a larger simulation. For increased parallelism (up to 8 patches) add one or more of "twoAwayX yes", "twoAwayY yes", and "twoAwayZ yes" to the config file.
Interactive BPTI (882 atoms, small) (README, config, directory, 56k .tar.gz, 54k .zip)
ER-GRE benchmark (36573 atoms, spherical) (config, directory, 1.1M .tar.gz, 1.0M .zip)
decalanin (66 atoms, tiny, ancient) (config, directory, .tar.gz, .zip)
Tcl forces (decalanin) (config, directory, .tar.gz, .zip)

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